Variant report

Variant	rs3786539
Chromosome Location	chr19:42366232-42366233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
2	chr19:42351673..42358248-chr19:42360570..42366998,12	K562	blood:
3	chr19:42333324..42335444-chr19:42364379..42366261,2	K562	blood:
4	chr19:42365213..42368096-chr19:42429393..42431288,2	K562	blood:
5	chr19:42361938..42366462-chr19:42459916..42465209,13	K562	blood:
6	chr19:42333324..42335444-chr19:42363709..42366261,3	K562	blood:
7	chr19:42366028..42368892-chr19:42439399..42440962,2	MCF-7	breast:
8	chr19:42366038..42367665-chr19:42439832..42441415,2	K562	blood:
9	chr19:42362818..42366371-chr19:42406679..42410305,7	MCF-7	breast:
10	chr19:42362719..42367011-chr19:42578185..42581831,5	K562	blood:
11	chr19:42364213..42366472-chr19:42430072..42433705,3	K562	blood:
12	chr19:42245127..42247870-chr19:42365049..42367593,2	MCF-7	breast:
13	chr19:42362135..42368129-chr19:42461941..42464761,7	MCF-7	breast:
14	chr19:42361079..42367934-chr19:42431466..42436133,8	K562	blood:
15	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000076928	Chromatin interaction
ENSG00000269119	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000142025	Chromatin interaction
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11665965	0.83[MEX][hapmap]
rs12974044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864207	0.83[MEX][hapmap]
rs2075751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752172	1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs7258162	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3786539	TMEM143	cis	parietal	SCAN
rs3786539	PSG3	cis	multi-tissue	Pritchard
rs3786539	PSG9	cis	multi-tissue	Pritchard
rs3786539	SLC1A5	cis	parietal	SCAN
rs3786539	CEACAM3	cis	multi-tissue	Pritchard
rs3786539	IGFL1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42364400-42367600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
2	chr19:42364600-42366800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr19:42364600-42366800	Transcr. at gene 5' and 3'	HMEC	breast
4	chr19:42364600-42367600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:42364600-42367800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr19:42364600-42367800	Transcr. at gene 5' and 3'	A549	lung
7	chr19:42364600-42368800	Transcr. at gene 5' and 3'	Dnd41	blood
8	chr19:42364600-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:42364800-42366600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
10	chr19:42364800-42367000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:42364800-42367000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:42364800-42367000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
13	chr19:42364800-42367200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
14	chr19:42364800-42367200	Transcr. at gene 5' and 3'	K562	blood
15	chr19:42364800-42367200	Transcr. at gene 5' and 3'	NHEK	skin
16	chr19:42364800-42367400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:42364800-42367600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
18	chr19:42364800-42367600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
19	chr19:42364800-42367600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:42364800-42367600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:42364800-42367800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:42364800-42367800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
23	chr19:42364800-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:42365000-42366600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:42365000-42366800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:42365000-42367000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:42365000-42367000	Transcr. at gene 5' and 3'	NHLF	lung
28	chr19:42365000-42367000	Transcr. at gene 5' and 3'	Osteobl	bone
29	chr19:42365000-42367600	Transcr. at gene 5' and 3'	HepG2	liver
30	chr19:42365200-42366400	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:42365200-42366600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:42365200-42366800	Transcr. at gene 5' and 3'	NH-A	brain
33	chr19:42365200-42367000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
34	chr19:42365200-42367200	Transcr. at gene 5' and 3'	HSMM	muscle
35	chr19:42365200-42367200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
36	chr19:42365200-42367400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
37	chr19:42365200-42367400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:42365200-42368800	Genic enhancers	Spleen	Spleen
39	chr19:42365200-42369600	Transcr. at gene 5' and 3'	Hela-S3	cervix
40	chr19:42365400-42366400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
41	chr19:42365400-42366400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
42	chr19:42365400-42366400	Enhancers	Ovary	ovary
43	chr19:42365400-42366800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr19:42365400-42367000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
45	chr19:42365400-42367400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
46	chr19:42365400-42367600	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:42365400-42367800	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr19:42365400-42369200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr19:42365400-42369800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:42365400-42374800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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